In RGLab/HIPCCyto: HIPC Cytometry

knitr::opts_chunk$set(echo = FALSE, message = FALSE)

library(flowWorkspace)
library(ggcyto)

gs_dir <- params$gs_dir
gate <- "Lymphocytes"
gs <- load_gs(file.path(gs_dir, "gs"))
original_gates <- readRDS(file.path(gs_dir, sprintf("%s_original.RDS", gate)))

parent_gate <- basename(gs_pop_get_parent(gs, gate))
pd <- pData(gs)
imputed <- pd$name[pd$imputed == "TRUE"]

imputed_gs <- gs[imputed]
imputed_gates <- gs_pop_get_gate(imputed_gs, gate)
original_gates <- original_gates[imputed]

The red gates are the original gates, and the black gates are the imputed gates.

plots <- lapply(imputed_gs, function(gh) {
  print(sampleNames(gh))
  cf <- gh_pop_get_data(gh, parent_gate)
  p <- ggcyto(cf, aes(x = "FSC-A", y = "SSC-A")) +
    geom_hex() +
    geom_gate(original_gates, colour = "red", size = 1) +
    geom_gate(imputed_gates, colour = "black", size = 1)
  print(p)
})